Object Stack Collapse
I found something helpful to deal with the modifier stack issue when dealing with UVs (issue #1). Inside of the UV editor, under the [N] key panel, within the "View" tab, under "Overlays", there is a checkbox called "Modified" which shows the end result of modifiers.

So if you use the "offset" features of the array and mirror modifiers, the duplicated geometry will show up in the UV editor as faded gray lines. Extremely helpful!

Seems like this box should be checked by default.

So the thing I'm most concerned with is dealing with multiple sub-objects of simple larger objects. When those sub-objects have modifiers applied to them. It would be great to have some way to combine these together automatically or quickly for exporting.